Package: BAMBI 2.3.5

BAMBI: Bivariate Angular Mixture Models

Fit (using Bayesian methods) and simulate mixtures of univariate and bivariate angular distributions. Chakraborty and Wong (2021) <doi:10.18637/jss.v099.i11>.

Authors:Saptarshi Chakraborty, Samuel W.K. Wong

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# Install 'BAMBI' in R:
install.packages('BAMBI', repos = c('https://c7rishi.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/c7rishi/bambi/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • tim8 - Backbone Dihedral Angles of Triose Phosphate Isomerase
  • wind - Saturna Island wind directions

On CRAN:

49 exports 3 stars 1.67 score 51 dependencies 1 dependents 2 mentions 63 scripts 545 downloads

Last updated 2 years agofrom:08a5ad9b2e. Checks:OK: 4 NOTE: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 03 2024
R-4.5-win-x86_64NOTESep 03 2024
R-4.5-linux-x86_64NOTESep 03 2024
R-4.4-win-x86_64NOTESep 03 2024
R-4.4-mac-x86_64NOTESep 03 2024
R-4.4-mac-aarch64NOTESep 03 2024
R-4.3-win-x86_64OKSep 03 2024
R-4.3-mac-x86_64OKSep 03 2024
R-4.3-mac-aarch64OKSep 03 2024

Exports:add_burnin_thinangmcmcbestcriterionbestmodelcirc_corcirc_varcor_modelcontour_modeld_fittedDICdvmdvmcosdvmcosmixdvmmixdvmsindvmsinmixdwnormdwnorm2dwnorm2mixdwnormmixextractsamplesfit_angmixfit_incremental_angmixfit_vmcosmixfit_vmmixfit_vmsinmixfit_wnorm2mixfit_wnormmixfix_labelis.angmcmclatent_allocationlpdtraceminuspi_to_piparamtracepointestr_fittedrvmrvmcosrvmcosmixrvmmixrvmsinrvmsinmixrwnormrwnorm2rwnorm2mixrwnormmixselect_chainssurface_modelvm2_mlezero_to_2pi

Dependencies:abindbackportsbridgesamplingBrobdingnagcheckmateclicodacodetoolscolorspacecombinatdigestdistributionalfansifarverfuturefuture.applygenericsglobalsgluegtoolslabel.switchinglabelinglatticelifecyclelistenvloolpSolvemagrittrMatrixmatrixStatsmunsellmvtnormnumDerivparallellypillarpkgconfigposteriorqrngR6RColorBrewerRcppRcppArmadillorlangscalesstringistringrtensorAtibbleutf8vctrsviridisLite

Readme and manuals

Help Manual

Help pageTopics
Add (extra) burnin and thin to angmcmc object after original runadd_burnin_thin
Create an mcmc.list object from an angmcmc objectas.mcmc.list.angmcmc
'BAMBI': An R package for Bivariate Angular Mixture ModelsBAMBI
Convenience function for extracting angmcmc object, and the value of the model selection criterion corresponding to the best fitted model in stepwise fitsbestcriterion bestmodel
Log Marginal Likelihood via Bridge Sampling for angmcmc objectsbridge_sampler.angmcmc
Sample circular correlation coefficientscirc_cor
Analytic circular variances and correlations for bivariate angular modelscirc_varcor_model
Contourplot for bivariate angular mixture model densitiescontour_model
Contour plot for angmcmc objects with bivariate datacontour.angmcmc
Density and random deviates from an angmcmc objectd_fitted r_fitted
Density plots for angmcmc objectsdensityplot.angmcmc
Deviance Information Criterion (DIC) for angmcmc objectsDIC
Extract MCMC samples for parameters from an angmcmc objectextractsamples
Fitting Bivariate and univariate angular mixture modelsfit_angmix
Stepwise fitting of angular mixture models with incremental component sizes and optimum model selectionfit_incremental_angmix
Fitting bivariate von Mises cosine model mixtures using MCMCfit_vmcosmix
Fitting univariate von Mises mixtures using MCMCfit_vmmix
Fitting bivariate von Mises sine model mixtures using MCMCfit_vmsinmix
Fitting bivariate wrapped normal model mixtures using MCMCfit_wnorm2mix
Fitting univariate wrapped normal mixtures using MCMCfit_wnormmix
Fix label switching in angmcmc objectsfix_label
Angular MCMC ('angmcmc') Objectangmcmc is.angmcmc
Finding latent allocation (component indicators) from an angmcmc objectlatent_allocation
Extract Log-Likelihood from angmcmc objectslogLik.angmcmc
Leave-one-out cross-validation (LOO) for angmcmc objectsloo.angmcmc
Trace and autocorrelation plots of log posterior density or log likelihood from an angmcmc objectlpdtrace
Trace plot for parameters from an angmcmc objectparamtrace
Summary plots for angmcmc objectsplot.angmcmc
Point estimates for parameters from an angmcmc objectpointest
Quantile estimates for parameters from an angmcmc objectquantile.angmcmc
The univariate von Mises distributiondvm rvm
The bivariate von Mises cosine modeldvmcos rvmcos
The bivariate von Mises cosine model mixturesdvmcosmix rvmcosmix
The univariate von Mises mixturesdvmmix rvmmix
The bivariate von Mises sine modeldvmsin rvmsin
The bivariate von Mises sine model mixturesdvmsinmix rvmsinmix
The univariate Wrapped Normal distributiondwnorm rwnorm
The bivariate Wrapped Normal distributiondwnorm2 rwnorm2
The bivariate Wrapped Normal mixturesdwnorm2mix rwnorm2mix
The univariate Wrapped Normal mixturesdwnormmix rwnormmix
Select chains from angmcmc objectsselect_chains
Summary statistics for parameters from an angmcmc objectsummary.angmcmc
Surface for bivariate angular mixture model densitiessurface_model
Backbone Dihedral Angles of Triose Phosphate Isomerase (8TIM)tim8
Maximum likelihood estimation of bivariate von Mises parametersvm2_mle
Watanabe-Akaike Information Criterion (WAIC) for angmcmc objectswaic.angmcmc
Saturna Island wind directionswind
Wrap angles into '[-pi, pi]' or '[0, 2*pi]'minuspi_to_pi zero_to_2pi